Research Tools

JBEI-ICE

ICE: A cloud-based freely open-source repository with physical sample tracking capabilities that stores microbial strain, sequence, and plant seed information, including that associated with JBEI publications. Includes features such as DNA sequence editing and annotation, sequence validation results analysis, FASTA/GenBank/SBOL 2 support, and Web-of-Registries functionality.

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VectorEditor: A cloud-based freely open-source visual DNA editing and annotation tool.

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DeviceEditor: A cloud-based SBOL Visual-compliant biological computer-aided design canvas that serves as a front-end for j5.

j5

j5: A cloud-based DNA assembly protocol design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods. j5 identifies assembly incompatibilities and designs mitigation strategies accordingly, and performs cost-optimal design, leveraging DNA synthesis. Read more.

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PR-PR: A cloud-based freely open-source laboratory automation programming platform that allows researchers to time-effectively use liquid-handling robots and microfluidic devices. After minimal training, biologists can independently write complicated protocols within an hour. Read more.

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Experiment Data Depot (EDD): A cloud-based freely open-source experiment data repository that stores proteomics, metabolomics, transcriptomics, flow cytometry, plate reader, and BioLector digital data, including that associated with JBEI publications.

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Arrowland: A cloud-based interactive tool for visualizing functional genomics data (fluxomics, metabolomics, proteomics, transcriptomics).

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MASCP Gator is a proteomics aggregation utility  that queries and aggregates information from a variety of online Arabidopsis proteomic resources.

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1001 Proteomes is a portal providing a simple way to browse changes to proteins caused by non-synonymous single nucleotide polymorphisms (nsSNPs) in accessions or natural strains of Arabidopsis thaliana.

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Plant Protein Alignment and Phosphorylation Resource PPAPR shows both observed and predicted phosphorylation sites with an alignment of related sequences so you can see what sites are conserved and whether phosphorylation at a homologous site is observed or predicted.

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Technoeconomic Model Wiki JBEI is developing technoeconomic models of various aspects of lignocellulosic biofuel production. The models can be used to estimate the impact of various market and technology developments on the economics of biofuel and enzyme production.  The models and the assumptions used to construct them have been deposited on the wiki, which allows users to choose the parameter scenarios that are of most interest to them. Read more.

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RiceNet is a probabilistic functional gene network for 41,203 non-TE related genes of Oryza sativa (by TIGR release 5), constructed using a modified Bayesian integration of many different data types from several different organisms, with each data type weighted according to how well it links genes that are known to function together in Oryza sativa.

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Rice GT Database The Rice GT Database was created to integrate and host functional genomic information for all putative rice Glycosyltransferases (GTs), as a part of Joint BioEnergy Institute (JBEI).

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Rice Glycosyl Hydrolase Database was created to integrate and host functional genomic information for all putative rice Glycoside hydrolases (GHs), as a part of Joint BioEnergy Institute (JBEI).

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Rice Kinase Database The Rice Kinase Database was created to host functional genomic information gathered as part of an NSF funded rice kinase proteomics project and subsequently updated, expanded and maintained by JBEI.

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Rice Oligonucleotide Array Database (ROAD) is a public resource for gene expression and coexpression analysis in rice, the most important staple food over the world. Over 1,000 microarray slides were incorporated and several kinds of analysis tools are available in ROAD.

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Directory of Databases for Plant Cell Wall-Related Enzymes The Directory of Databases for Plant Cell Wall-Related Enzymes is a companion database of our review paper “A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes” submitted to BioEnergy Research.

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JBEI GT Collection The JBEI GT Collection, the first glycosyltransferase clone collection specifically targeted for the study of plant cell wall biosynthesis, is expected to drive basic scientific understanding of GTs and better enable the manipulation of plant cell walls for the production of biofuels and other chemical products.

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KitBase A publicly available open-source platform for over 1500 whole-genome sequenced mutants in Kitaake. Kitaake is a fast generation rice variety (<3 months from seed to seed) that facilitates studies of grass genes controlling cell wall biosynthesis and modification. KitBase offers users the ability to search the database using BLAST and gene IDs, visualize mutations using JBrowser, and download genomic and phenotypic data.

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MaxBin: a software package used for binning assembled metagenomic sequences, based on an Expectation-Maximization algorithm. MaxBin allows users to understand the underlying genomes of the microbes in their metagenomes by providing assembled metagenomic sequences and the reads coverage information or sequencing reads. MaxBin will report genome-related statistics, including the estimated completeness, GC content, and genome size. Users can then use MEGAN or similar software to find the taxonomy of each bin.

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Targeted Proteomic toolkit for Escherichia coli proteins To expand the utility of quantitative proteomics for metabolic engineering, we validated and optimized targeted proteomics methods for over 400 proteins from more than 20 major pathways in E. coli metabolism (Batth TS, et al., 2014). Complementing these methods, we constructed a series of synthetic genes to produce concatenated peptides (QconCAT) for absolute quantification of the proteins and made them available through the Addgene plasmid repository.